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Acute pneumonia is the leading cause of childhood morbidity and mortality, especially in children with an inherited or therapeutically induced immunodeficiency. In a majority of cases, the pathogen(s) responsible for the disease remains unknown even following comprehensive testing.We assembled a cohort of hospitalized children with community-acquired pneumonia of unknown etiology, immunocompromised or not, and collected blood and bronchoalveolar lavage samples. Using optimized sample preparation, untargeted Next Generation Sequencing and dedicated bioinformatics pipelines, we will identify the viral, bacterial and fungal microbiota associated with disease. We will compare this microbiota in immunocompromised and immunocompetent children. In case of identification of new viruses, we will use molecular tools to get the full viral genome sequence. This clinical metagenomics approach of this very severe clinical condition will pave the way to a better understanding of immunological responses and to a better management of children suffering acute pneumonia.

Qualifications

We are looking for a skilled and competent molecular biologist with if possible experience in DNA sequencing and interpretation of results of metagenomics data. The position is for 3 years.